I don't know nearly as much about the Philippines as I wish I did; and unfortunately I'm out of my office, but here are a few books that leap to mind which I have used and came well recommended by colleagues who work on the Philippines.

• Benedict Anderson, "Under Three Flags: Anarchism and the Anti-colonial Imagination"- in usual Anderson style the book concerns the rise of national identity in the Philippines, especially its genesis in writing/intellectual circles. So this book mostly covers pre-American colonialism.

• Warwick Anderson, "Colonial Pathologies: American Tropical Medicine, Race, and Hygiene in the Philippines"- part of a pretty well developed corpus of works on colonialism as seen through public health/sanitation policies. About the American administration and covers some of the ways health was used to control/"civilize" peoples.

• Matt Matsuda, "Pacific Worlds" - not strictly Philippine history; but one that covers South East Asia, the Island Pacific, and the Pacific Rim- so if you want a long view of the region and to see how the Philippines has connected to it, this book can be a useful introduction.

• Andrew Peterson, "Making the First Global Trade Route: Indo Contributions and Spanish Dependency in the Forging of the Acapulco-Manila Gallon Trade, 1519-1650" - this is a dissertation rather than a published monograph, so if you have access to ProQuest it shouldn't be hard to get- but it covers the early Spanish colonization and the Galleon trade; essentially discussing the ways in which the Filipinos were key to the Spanish success because they knew the islands and the Spanish hadn't a clue what they were doing for a long time.